Raw Data

suppressMessages(require(knitr, quietly = T))
suppressMessages(require(kableExtra, quietly = T))
suppressMessages(require(rmarkdown, quietly = T))
suppressMessages(require(plyr, quietly = T))
suppressMessages(require(dplyr, quietly = T))
suppressMessages(require(ggplot2, quietly = T))
suppressMessages(require(GGally, quietly = T))

load("data.RData")

kable(df, 
      digits = 3,
      row.names = T,
      caption = "Raw data") %>%
    kable_styling(bootstrap_options = c("striped", "hover", "condensed", "responsive"),
                  font_size = 10) %>%
    scroll_box(width = "100%", height = "300px")
Raw data
PatientID Age AgeGreater60 Sex LowIntermacs InterMACS RVAD Sensitized VAD Indication Device Type Survival Outcome Time num Total PBMC num lymph lymph live lymph CD3 of live lymph CD19 of live lymph CD19+CD27- CD19+CD27+ CD27+38++plasma blasts CD27-38++ transitional CD27-IgD+ mature naive CD27+IgD- switched memory CD27-IgD- switched memory CD27+IgD+ unswitched memory CD27+IgD-IgM+ switched memory CD27+IgD+IgM+ nonswitched memory CD19+27+IgG+IgM- memory CD19+24dim38dim naive mature CD19+24+38++transitional CD19CD24hiCD38-memory CD19+27-38+CD5+transitionals CD19+CD268+ CD268 of +27-38++transitional CD19+CD11b+ CD19+CD5+ CD19+CD27+CD24hi CD19+CD5+CD24hi CD19+CD5+CD11b+ CD19+27+IgD-38++IgG ASC
1 15 70 older Female High 2 No NA DT HMII alive Alive 0 86135 70306 81.62 93.71 74.50 1.59 61.74 38.26 1.91 2.67 33.97 14.50 26.81 24.71 20.67 62.47 9.03 73.00 2.00 24.71 1.27 20.23 71.43 0.48 12.79 0.38 3.24 0.48 4.60
2 15 70 older Female High 2 No NA DT HMII alive Alive 1 81004 41334 51.03 94.06 53.64 2.99 61.70 38.30 3.10 2.75 39.07 13.34 22.12 25.47 12.58 63.11 15.99 78.92 2.93 17.38 3.35 23.24 71.88 0.52 11.70 0.09 1.29 0.52 9.83
3 15 70 older Female High 2 No NA DT HMII alive Alive 3 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA
4 15 70 older Female High 2 No NA DT HMII alive Alive 5 90024 39434 43.80 95.32 68.83 5.62 71.59 28.41 0.85 1.66 35.23 13.02 35.80 15.96 22.94 52.37 5.85 76.42 1.14 21.83 0.62 14.54 48.57 0.38 4.69 0.00 0.80 0.38 0.62
5 15 70 older Female High 2 No NA DT HMII alive Alive 8 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA
6 15 70 older Female High 2 No NA DT HMII alive Alive 14 106791 80532 75.41 88.82 79.92 1.57 62.32 37.68 1.70 4.02 28.04 22.86 34.11 15.00 23.92 39.41 15.03 61.61 3.66 34.55 1.97 20.36 73.33 0.80 8.57 0.27 1.79 0.98 0.71
7 15 70 older Female High 2 No NA DT HMII alive Alive 21 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA
8 22 67 older Male High 2 Yes NA BTT HMII dead Died 0 129980 41600 32.00 91.40 39.03 2.85 49.63 50.37 7.02 11.55 28.37 29.11 20.79 21.72 19.43 28.34 9.80 69.59 4.90 20.33 6.13 31.15 33.60 20.15 22.27 0.28 4.25 16.54 2.09
9 22 67 older Male High 2 Yes NA BTT HMII dead Died 1 59478 20182 33.93 89.07 44.50 10.08 60.93 39.07 2.10 2.70 42.88 13.69 17.66 25.77 13.06 46.12 3.13 81.35 1.16 16.11 0.83 37.58 6.12 5.52 11.64 0.06 1.49 2.76 4.07
10 22 67 older Male High 2 Yes NA BTT HMII dead Died 3 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA
11 22 67 older Male High 2 Yes NA BTT HMII dead Died 5 26646 9754 36.61 98.69 58.32 7.57 64.88 35.12 2.06 0.55 46.50 12.62 17.70 23.18 15.07 53.31 12.50 83.40 1.10 15.64 1.76 28.12 0.00 7.54 16.46 0.55 1.92 6.04 13.00
12 22 67 older Male High 2 Yes NA BTT HMII dead Died 8 73641 21944 29.80 96.79 48.91 4.47 62.74 37.26 2.84 3.16 37.47 17.79 24.95 19.79 19.46 38.11 9.46 79.79 1.89 13.58 1.24 27.05 20.00 14.11 13.37 0.21 2.74 10.53 3.31
13 22 67 older Male High 2 Yes NA BTT HMII dead Died 14 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA
14 22 67 older Male High 2 Yes NA BTT HMII dead Died 21 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA
15 14 39 younger Female Low 3 Yes No BTT HMII dead Died post OHT 0 52016 30920 59.44 95.77 55.57 24.62 58.73 41.27 2.14 0.97 53.01 5.05 5.45 36.50 9.39 81.29 2.88 81.48 5.65 9.02 0.48 97.75 71.83 0.67 22.89 0.34 1.78 0.49 NA
16 14 39 younger Female Low 3 Yes No BTT HMII dead Died post OHT 1 75516 48801 64.62 92.13 52.90 18.64 70.39 29.61 2.92 2.21 62.18 5.13 7.98 24.70 13.79 69.54 3.19 84.14 3.64 6.36 0.41 94.93 43.78 0.57 15.61 0.23 0.91 0.36 NA
17 14 39 younger Female Low 3 Yes No BTT HMII dead Died post OHT 3 250612 130454 52.05 95.75 60.05 3.29 46.04 53.96 1.34 3.89 33.08 32.47 8.29 26.15 3.56 34.61 0.09 76.71 0.39 13.20 0.28 39.79 14.38 2.26 1.56 10.45 2.89 3.04 0.08
18 14 39 younger Female Low 3 Yes No BTT HMII dead Died post OHT 5 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA
19 14 39 younger Female Low 3 Yes No BTT HMII dead Died post OHT 8 212478 120477 56.70 85.12 48.36 12.51 79.57 20.43 1.35 2.14 58.73 12.87 18.44 9.96 5.63 34.32 0.11 86.74 0.41 6.88 0.15 35.30 53.09 1.23 0.75 2.36 1.04 1.47 NA
20 14 39 younger Female Low 3 Yes No BTT HMII dead Died post OHT 14 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA
21 14 39 younger Female Low 3 Yes No BTT HMII dead Died post OHT 21 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA
22 3 58 younger Male Low 3 Yes No BTT HMII alive Alive s/p OHT 0 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA
23 3 58 younger Male Low 3 Yes No BTT HMII alive Alive s/p OHT 1 246811 86529 35.06 93.49 67.96 17.48 81.66 18.34 2.05 6.85 51.33 13.69 29.91 5.08 15.68 5.94 0.19 61.95 0.76 13.51 4.07 92.62 34.06 6.90 12.07 8.00 2.54 3.85 0.26
24 3 58 younger Male Low 3 Yes No BTT HMII alive Alive s/p OHT 3 406771 90343 22.21 97.34 49.28 17.02 75.04 24.96 4.47 18.36 28.45 21.86 46.07 3.62 24.97 4.33 0.13 47.41 1.64 19.70 18.15 72.76 8.08 25.69 28.35 13.95 4.66 19.20 0.41
25 3 58 younger Male Low 3 Yes No BTT HMII alive Alive s/p OHT 5 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA
26 3 58 younger Male Low 3 Yes No BTT HMII alive Alive s/p OHT 8 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA
27 3 58 younger Male Low 3 Yes No BTT HMII alive Alive s/p OHT 14 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA
28 3 58 younger Male Low 3 Yes No BTT HMII alive Alive s/p OHT 21 330191 81636 24.72 94.57 45.14 14.70 70.51 29.49 8.94 16.23 38.92 23.53 30.83 6.72 23.93 7.07 0.18 46.63 2.35 16.12 8.59 74.45 39.90 24.19 21.18 12.62 3.26 12.93 0.38
29 20 75 older Male High 2 No NA DT HMII alive Alive 0 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA
30 20 75 older Male High 2 No NA DT HMII alive Alive 1 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA
31 20 75 older Male High 2 No NA DT HMII alive Alive 3 121794 28129 23.10 97.05 52.79 16.42 70.08 29.92 0.29 0.54 50.71 21.46 22.96 4.86 34.18 12.51 23.49 39.78 0.31 55.18 0.35 96.01 16.67 1.74 5.27 23.38 2.95 1.00 0.10
32 20 75 older Male High 2 No NA DT HMII alive Alive 5 82157 17295 21.05 99.20 72.54 7.41 68.21 31.79 1.10 0.55 48.47 22.90 23.60 5.04 31.90 13.57 18.10 37.84 0.47 56.73 0.35 92.37 14.29 2.05 7.79 26.20 4.72 1.42 1.02
33 20 75 older Male High 2 No NA DT HMII alive Alive 8 154810 27067 17.48 98.04 72.18 5.03 74.91 25.09 0.90 1.65 58.05 14.76 20.82 6.37 23.43 25.71 22.57 44.94 0.60 49.36 0.71 86.59 22.73 3.30 7.64 20.15 4.87 1.72 0.00
34 20 75 older Male High 2 No NA DT HMII alive Alive 14 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA
35 20 75 older Male High 2 No NA DT HMII alive Alive 21 197936 15446 7.80 95.86 50.35 5.44 79.13 20.87 3.98 3.11 52.30 15.90 29.81 1.99 20.23 5.78 24.86 40.62 1.12 50.06 1.89 62.36 8.00 7.20 9.94 13.17 3.60 5.09 1.55
36 24 64 older Male High 2 No Yes BTT HMII alive Alive s/p OHT 0 59881 8971 14.98 97.40 50.06 9.57 75.84 24.16 3.59 8.13 64.83 13.40 15.67 6.10 19.31 18.81 16.83 76.67 6.10 6.82 2.00 88.16 47.06 10.53 11.24 10.41 9.93 6.94 11.93
37 24 64 older Male High 2 No Yes BTT HMII alive Alive s/p OHT 1 60193 23874 39.66 96.72 58.83 16.24 80.37 19.63 1.87 3.31 68.58 10.62 14.72 6.08 21.33 22.83 3.80 80.61 3.63 8.03 0.33 94.16 57.26 2.96 5.01 10.19 4.72 1.41 1.24
38 24 64 older Male High 2 No Yes BTT HMII alive Alive s/p OHT 3 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA
39 24 64 older Male High 2 No Yes BTT HMII alive Alive s/p OHT 5 135335 27834 20.57 97.35 44.75 5.61 63.22 36.78 8.49 17.63 39.01 23.16 30.72 7.11 17.53 10.38 12.16 42.70 4.93 19.28 4.68 67.37 4.10 26.64 17.76 19.21 14.54 14.47 10.60
40 24 64 older Male High 2 No Yes BTT HMII alive Alive s/p OHT 8 247113 62042 25.11 96.41 43.93 14.82 78.42 21.58 2.52 5.24 65.35 12.22 17.53 4.90 20.39 17.20 2.93 77.86 2.11 8.78 2.94 84.64 9.70 10.64 13.93 9.90 11.59 8.48 3.51
41 24 64 older Male High 2 No Yes BTT HMII alive Alive s/p OHT 14 142053 56983 40.11 93.01 62.72 12.87 85.10 14.90 0.69 1.64 68.02 8.40 21.03 2.55 17.03 13.68 1.08 83.33 0.37 7.38 0.26 79.00 16.07 3.01 5.85 5.16 5.24 1.77 0.70
42 24 64 older Male High 2 No Yes BTT HMII alive Alive s/p OHT 21 60384 17029 28.20 93.65 40.96 21.36 83.80 16.20 1.47 2.32 63.52 9.69 23.80 2.99 23.55 15.58 0.91 78.16 1.09 8.13 1.00 83.65 17.72 4.70 8.42 5.99 7.22 3.76 1.56
43 6 43 younger Male High 2 Yes No BTT HMII alive Alive s/p OHT 0 515760 266115 51.60 96.30 69.66 8.57 72.22 27.78 6.26 4.77 43.09 26.01 28.26 2.63 16.67 2.67 28.25 50.35 0.41 12.78 4.47 84.76 19.47 9.56 4.55 8.29 0.87 2.18 0.75
44 6 43 younger Male High 2 Yes No BTT HMII alive Alive s/p OHT 1 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA
45 6 43 younger Male High 2 Yes No BTT HMII alive Alive s/p OHT 3 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA
46 6 43 younger Male High 2 Yes No BTT HMII alive Alive s/p OHT 5 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA
47 6 43 younger Male High 2 Yes No BTT HMII alive Alive s/p OHT 8 539521 223872 41.49 96.72 60.02 12.63 80.13 19.87 1.66 2.48 43.56 19.52 35.24 1.68 20.46 3.67 20.54 55.76 0.18 10.80 2.43 87.82 13.25 6.55 5.96 4.65 0.95 2.51 0.65
48 6 43 younger Male High 2 Yes No BTT HMII alive Alive s/p OHT 14 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA
49 6 43 younger Male High 2 Yes No BTT HMII alive Alive s/p OHT 21 564317 216312 38.33 97.40 55.80 4.83 74.19 25.81 5.35 5.77 37.90 25.72 34.76 1.62 17.99 2.18 31.75 61.61 0.77 13.44 6.97 76.55 6.97 10.34 11.14 4.46 0.94 5.14 2.43
50 5 65 older Female High 2 No Yes BTT HMII alive Alive s/p OHT 0 1073919 336538 31.34 100.00 63.29 14.80 93.05 6.95 0.73 8.05 75.49 4.55 19.16 0.80 7.25 8.78 28.04 88.72 2.51 5.18 1.02 90.49 68.18 2.32 4.09 1.69 3.48 1.27 5.78
51 5 65 older Female High 2 No Yes BTT HMII alive Alive s/p OHT 1 270301 97229 35.97 91.63 18.43 61.67 97.68 2.32 0.20 5.85 69.45 1.63 28.19 0.73 27.57 21.43 17.05 84.32 7.26 2.73 0.84 99.44 97.60 0.54 2.64 1.51 3.63 0.29 3.40
52 5 65 older Female High 2 No Yes BTT HMII alive Alive s/p OHT 3 499016 78019 15.63 89.41 25.83 51.38 92.98 7.02 0.32 4.66 51.34 6.31 41.59 0.76 36.49 5.96 22.81 73.48 6.73 7.93 0.33 98.78 96.52 1.31 2.06 5.19 2.68 0.59 2.45
53 5 65 older Female High 2 No Yes BTT HMII alive Alive s/p OHT 5 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA
54 5 65 older Female High 2 No Yes BTT HMII alive Alive s/p OHT 8 115825 32513 28.07 91.04 44.61 15.76 80.52 19.48 4.16 7.82 49.91 18.37 30.52 1.20 14.87 3.33 30.19 61.08 8.70 12.56 1.58 89.80 76.71 2.87 6.07 11.12 8.08 1.59 1.17
55 5 65 older Female High 2 No Yes BTT HMII alive Alive s/p OHT 14 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA
56 5 65 older Female High 2 No Yes BTT HMII alive Alive s/p OHT 21 407080 97651 23.99 91.29 66.96 12.20 84.66 15.34 2.88 5.60 61.89 13.73 22.65 1.74 20.16 7.23 29.39 68.49 5.28 10.60 1.17 92.50 54.35 3.48 6.53 9.61 8.34 1.85 2.83
57 23 68 older Male High 2 No No BTT HMII alive Alive s/p OHT 0 44004 20612 46.84 43.65 15.61 21.54 49.64 50.36 10.37 0.57 15.94 45.15 33.18 5.73 24.69 5.68 20.25 44.58 1.55 36.17 0.88 67.23 27.27 32.35 15.48 20.02 4.49 10.94 2.76
58 23 68 older Male High 2 No No BTT HMII alive Alive s/p OHT 1 99731 23424 23.49 91.81 41.33 10.89 35.24 64.76 11.83 1.62 18.71 59.21 16.19 5.89 28.16 5.89 18.53 39.98 4.66 42.16 2.33 84.07 2.63 22.55 15.21 40.28 6.07 9.70 3.96
59 23 68 older Male High 2 No No BTT HMII alive Alive s/p OHT 3 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA
60 23 68 older Male High 2 No No BTT HMII alive Alive s/p OHT 5 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA
61 23 68 older Male High 2 No No BTT HMII alive Alive s/p OHT 8 129637 50001 38.57 90.65 44.41 6.05 30.66 69.34 17.12 4.05 10.62 66.50 19.60 3.28 26.41 3.46 13.37 39.74 7.15 39.49 11.91 71.97 2.70 32.48 33.14 43.91 7.81 22.70 3.82
62 23 68 older Male High 2 No No BTT HMII alive Alive s/p OHT 14 134368 46363 34.50 88.32 34.25 4.63 32.47 67.53 12.86 8.38 8.91 64.89 22.88 3.32 24.78 3.89 13.58 36.16 6.01 40.33 13.77 72.11 1.89 29.89 26.36 42.80 6.17 15.97 3.29
63 23 68 older Male High 2 No No BTT HMII alive Alive s/p OHT 21 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA
64 28 72 older Male Low 4 Yes NA BTT HMII dead Died 0 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA
65 28 72 older Male Low 4 Yes NA BTT HMII dead Died 1 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA
66 28 72 older Male Low 4 Yes NA BTT HMII dead Died 3 424375 21971 5.18 71.78 56.98 18.53 79.84 20.16 3.08 0.51 57.91 14.07 24.06 3.97 31.74 15.95 13.65 57.94 0.65 28.51 0.17 93.57 53.33 2.87 9.69 15.61 3.87 2.16 3.99
67 28 72 older Male Low 4 Yes NA BTT HMII dead Died 5 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA
68 28 72 older Male Low 4 Yes NA BTT HMII dead Died 8 177249 103442 58.36 76.40 15.43 5.64 65.13 34.87 5.21 0.20 35.56 27.91 31.90 4.62 26.60 8.28 13.24 67.89 0.29 20.13 0.00 78.60 22.22 5.50 16.09 25.56 6.80 4.73 0.89
69 28 72 older Male Low 4 Yes NA BTT HMII dead Died 14 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA
70 28 72 older Male Low 4 Yes NA BTT HMII dead Died 21 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA
71 18 37 younger Female High 2 Yes NA BTT PVAD dead Died s/p OHT 0 56374 12141 21.54 67.38 27.12 3.32 51.84 48.16 1.84 1.84 2.94 45.59 47.79 3.68 0.00 0.00 2.29 92.65 0.37 5.51 0.72 30.15 60.00 6.99 9.56 0.37 0.00 3.68 0.00
72 18 37 younger Female High 2 Yes NA BTT PVAD dead Died s/p OHT 1 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA
73 18 37 younger Female High 2 Yes NA BTT PVAD dead Died s/p OHT 3 7018 3464 49.36 89.03 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00
74 18 37 younger Female High 2 Yes NA BTT PVAD dead Died s/p OHT 5 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA
75 18 37 younger Female High 2 Yes NA BTT PVAD dead Died s/p OHT 8 80210 21828 27.21 85.74 20.38 3.50 61.98 38.02 8.55 2.90 5.50 34.96 56.18 3.36 0.00 0.00 3.21 89.31 0.61 2.60 1.49 23.66 0.00 21.37 9.16 1.07 0.15 5.34 1.31
76 18 37 younger Female High 2 Yes NA BTT PVAD dead Died s/p OHT 14 55068 19145 34.77 75.16 16.90 3.30 64.00 36.00 4.21 2.11 10.53 34.11 52.42 2.95 0.00 0.00 2.94 92.42 0.00 3.37 1.00 22.74 0.00 12.42 11.16 0.63 0.00 4.63 0.00
77 18 37 younger Female High 2 Yes NA BTT PVAD dead Died s/p OHT 21 76673 23615 30.80 83.39 26.27 2.06 63.55 36.45 5.42 5.42 5.17 34.48 58.13 2.22 0.00 0.00 2.72 89.41 0.00 3.45 1.95 18.23 4.55 18.23 8.87 1.23 0.25 4.68 0.00
78 10 36 younger Male High 2 Yes NA BTT PVAD alive Alive s/p OHT 0 481928 162052 33.63 99.70 64.73 5.05 3.91 96.09 8.89 1.34 0.72 94.99 3.14 1.15 4.07 0.84 0.32 90.28 2.84 1.58 1.27 6.82 9.17 14.61 90.11 4.95 5.71 13.01 0.51
79 10 36 younger Male High 2 Yes NA BTT PVAD alive Alive s/p OHT 1 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA
80 10 36 younger Male High 2 Yes NA BTT PVAD alive Alive s/p OHT 3 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA
81 10 36 younger Male High 2 Yes NA BTT PVAD alive Alive s/p OHT 5 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA
82 10 36 younger Male High 2 Yes NA BTT PVAD alive Alive s/p OHT 8 38113 21486 56.37 97.86 58.44 7.88 20.47 79.53 8.09 1.69 1.21 75.00 18.96 4.83 10.07 2.59 0.53 82.19 2.29 9.00 3.59 15.16 0.00 23.07 63.95 4.77 6.52 16.91 0.40
83 10 36 younger Male High 2 Yes NA BTT PVAD alive Alive s/p OHT 14 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA
84 10 36 younger Male High 2 Yes NA BTT PVAD alive Alive s/p OHT 21 80991 19210 23.72 99.00 50.61 3.50 12.33 87.67 14.74 4.81 1.05 85.41 11.13 2.41 8.48 0.52 1.56 80.00 8.27 3.76 7.41 13.68 0.00 30.83 77.74 10.83 14.14 19.85 2.81
85 21 30 younger Female Low 3 No Yes BTT HMII alive Alive s/p OHT 0 114586 35996 31.41 100.00 59.03 11.31 75.87 24.13 1.52 7.69 69.83 11.67 10.20 8.30 27.80 29.94 2.04 84.64 0.64 10.54 0.61 91.57 61.34 4.99 7.15 11.57 5.92 2.53 1.92
86 21 30 younger Female Low 3 No Yes BTT HMII alive Alive s/p OHT 1 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA
87 21 30 younger Female Low 3 No Yes BTT HMII alive Alive s/p OHT 3 349054 129419 37.08 95.25 62.35 8.81 79.64 20.36 2.72 4.45 57.70 13.93 25.89 2.48 57.14 13.49 8.69 74.29 3.76 12.35 1.41 85.87 62.53 3.41 5.43 7.67 1.40 1.92 1.06
88 21 30 younger Female Low 3 No Yes BTT HMII alive Alive s/p OHT 5 447309 176789 39.52 93.00 53.57 9.32 80.92 19.08 2.16 5.73 56.72 12.51 28.43 2.34 47.68 12.19 11.00 73.80 4.44 12.53 2.57 83.88 49.09 5.24 6.82 8.32 2.18 2.28 1.72
89 21 30 younger Female Low 3 No Yes BTT HMII alive Alive s/p OHT 8 558290 301468 54.00 95.62 47.73 7.04 79.13 20.87 3.43 7.49 53.19 13.48 30.32 3.01 36.36 14.54 12.10 70.55 5.15 11.89 3.51 79.79 52.89 6.98 8.50 7.82 1.92 3.09 1.96
90 21 30 younger Female Low 3 No Yes BTT HMII alive Alive s/p OHT 14 479402 362845 75.69 97.95 44.30 6.30 76.53 23.47 3.90 11.10 34.99 12.04 50.31 2.66 21.93 14.88 10.05 70.21 4.66 7.31 7.73 49.96 29.38 13.44 17.37 5.64 3.01 6.95 2.28
91 21 30 younger Female Low 3 No Yes BTT HMII alive Alive s/p OHT 21 334942 191418 57.15 93.28 70.35 4.04 70.89 29.11 6.20 17.70 56.45 19.57 20.44 3.53 38.91 14.64 10.35 55.11 6.61 14.34 8.70 80.96 58.92 7.58 7.96 10.11 2.08 2.08 2.48
92 8 43 younger Male Low 3 No No BTT HMII alive Alive s/p OHT 0 92221 27988 30.35 85.45 55.78 1.51 85.56 14.44 0.28 0.28 55.28 4.72 39.72 0.28 0.00 1.89 1.89 89.44 0.00 2.78 0.00 15.00 0.00 3.33 0.83 0.28 0.28 3.33 0.00
93 8 43 younger Male Low 3 No No BTT HMII alive Alive s/p OHT 1 273746 46755 17.08 93.25 50.14 7.57 88.27 11.73 0.09 2.12 54.52 3.36 42.00 0.12 8.40 6.87 0.00 92.00 0.12 3.45 0.00 3.94 11.43 1.12 0.64 2.76 0.33 2.15 0.00
94 8 43 younger Male Low 3 No No BTT HMII alive Alive s/p OHT 3 156053 71752 45.98 78.38 35.43 27.12 78.57 21.43 0.24 0.60 58.56 5.80 18.33 17.31 12.67 72.96 0.53 94.06 0.49 5.11 0.28 22.79 27.47 0.81 5.53 0.01 0.29 0.19 0.00
95 8 43 younger Male Low 3 No No BTT HMII alive Alive s/p OHT 5 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA
96 8 43 younger Male Low 3 No No BTT HMII alive Alive s/p OHT 8 156053 71752 45.98 78.38 35.43 27.12 78.57 21.43 0.24 0.60 58.56 5.80 18.33 17.31 12.67 72.96 0.53 94.06 0.49 5.11 0.28 22.79 27.47 0.81 5.53 0.01 0.29 0.19 0.00
97 8 43 younger Male Low 3 No No BTT HMII alive Alive s/p OHT 14 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA
98 8 43 younger Male Low 3 No No BTT HMII alive Alive s/p OHT 21 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA
99 16 63 older Male High 1 No NA BTT HMII dead Died 0 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA
100 16 63 older Male High 1 No NA BTT HMII dead Died 1 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA
101 16 63 older Male High 1 No NA BTT HMII dead Died 3 366713 77282 21.07 98.61 66.55 12.44 93.65 6.35 0.53 0.60 62.22 4.68 32.38 0.72 19.94 9.89 28.23 83.18 0.51 14.38 0.30 94.72 54.39 2.07 11.33 2.86 3.40 1.48 3.58
102 16 63 older Male High 1 No NA BTT HMII dead Died 5 262251 55344 21.10 99.55 62.37 14.39 93.00 7.00 1.03 0.69 65.71 4.74 28.37 1.17 25.93 17.28 25.93 79.87 1.20 17.05 0.48 97.76 58.18 2.27 11.13 4.12 4.91 1.87 6.10
103 16 63 older Male High 1 No NA BTT HMII dead Died 8 309193 61091 19.76 98.15 56.62 7.24 83.61 16.39 3.27 1.52 58.03 11.90 28.13 1.93 24.65 11.36 1.52 79.53 1.45 13.33 0.97 92.63 25.76 3.50 9.23 7.57 3.73 3.48 0.00
104 16 63 older Male High 1 No NA BTT HMII dead Died 14 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA
105 16 63 older Male High 1 No NA BTT HMII dead Died 21 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA
106 11 61 older Male High 2 No No BTT HMII alive Alive s/p OHT 0 411616 119210 28.96 90.82 73.63 5.88 74.30 25.70 2.80 6.46 57.94 19.20 18.72 4.13 19.10 15.42 15.30 53.51 13.78 25.19 0.21 47.23 53.77 5.75 5.92 22.63 3.46 2.55 0.74
107 11 61 older Male High 2 No No BTT HMII alive Alive s/p OHT 1 430509 79492 18.46 89.31 52.10 20.45 87.13 12.87 1.23 4.76 58.11 9.15 30.55 2.20 29.86 18.05 10.37 63.63 10.23 17.43 0.06 74.05 72.50 2.36 2.98 10.68 1.72 1.03 2.89
108 11 61 older Male High 2 No No BTT HMII alive Alive s/p OHT 3 395713 119670 30.24 97.90 23.79 6.27 82.17 17.83 0.79 1.99 49.95 13.01 33.91 3.13 28.36 16.83 5.00 56.33 7.13 26.73 0.02 79.50 82.88 1.96 5.55 16.30 3.61 1.88 0.42
109 11 61 older Male High 2 No No BTT HMII alive Alive s/p OHT 5 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA
110 11 61 older Male High 2 No No BTT HMII alive Alive s/p OHT 8 329840 73468 22.27 98.63 70.61 3.73 51.50 48.50 8.32 3.77 33.46 41.29 20.92 4.33 25.19 5.89 24.07 46.40 3.73 34.64 0.07 64.14 28.43 10.35 9.61 38.78 4.62 5.55 2.91
111 11 61 older Male High 2 No No BTT HMII alive Alive s/p OHT 14 350294 88823 25.36 97.63 74.37 4.37 73.35 26.65 4.91 4.83 56.54 21.32 19.84 2.30 34.68 11.25 18.37 61.98 5.78 20.55 0.04 63.91 47.54 6.81 6.17 21.77 2.90 2.74 3.00
112 11 61 older Male High 2 No No BTT HMII alive Alive s/p OHT 21 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA
113 4 67 older Male Low 3 No Yes BTT HVAD alive Alive s/p OHT 0 309890 41896 13.52 97.03 47.13 8.08 77.31 22.69 2.74 3.29 59.03 19.80 19.37 1.80 21.10 4.46 19.79 71.98 2.41 17.39 0.20 95.80 75.00 5.79 1.89 16.45 0.91 0.67 0.77
114 4 67 older Male Low 3 No Yes BTT HVAD alive Alive s/p OHT 1 274228 15653 5.71 97.85 35.76 28.87 51.45 48.55 2.60 2.13 30.85 43.13 22.77 3.26 20.09 3.92 30.51 57.58 1.31 28.20 0.18 91.23 59.57 12.08 2.04 34.44 0.38 0.16 0.16
115 4 67 older Male Low 3 No Yes BTT HVAD alive Alive s/p OHT 3 591939 57589 9.73 96.76 38.20 42.54 75.71 24.29 2.14 1.33 53.03 21.26 24.16 1.55 25.50 4.02 20.27 67.18 1.14 21.71 0.11 95.28 66.98 3.79 2.43 17.70 0.65 0.84 0.18
116 4 67 older Male Low 3 No Yes BTT HVAD alive Alive s/p OHT 5 189634 46711 24.63 97.74 34.84 37.32 75.30 24.70 0.70 0.55 46.97 22.05 30.28 0.70 23.67 1.56 31.44 73.33 0.75 18.59 0.00 84.61 86.17 3.44 2.11 18.68 0.94 0.63 0.69
117 4 67 older Male Low 3 No Yes BTT HVAD alive Alive s/p OHT 8 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA
118 4 67 older Male Low 3 No Yes BTT HVAD alive Alive s/p OHT 14 182319 40475 22.20 96.28 43.36 11.77 69.34 30.66 1.59 0.89 52.64 27.32 18.56 1.48 22.79 2.88 28.61 75.47 0.33 14.54 0.06 95.90 53.66 7.81 3.27 21.04 1.57 1.50 0.72
119 4 67 older Male Low 3 No Yes BTT HVAD alive Alive s/p OHT 21 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA
120 25 25 younger Female Low 3 No Yes BTT HMII alive Alive s/p OHT 0 47645 37377 78.45 94.61 2.47 9.41 78.56 17.02 1.71 4.63 34.94 16.09 44.77 4.21 4.35 28.99 59.42 67.26 3.10 26.22 7.50 72.82 53.90 13.50 28.20 3.04 7.70 7.67 0.96
121 25 25 younger Female Low 3 No Yes BTT HMII alive Alive s/p OHT 1 87452 43025 49.20 91.54 1.98 26.71 92.06 6.76 0.77 4.67 47.21 4.70 45.17 2.92 6.06 18.18 60.61 81.01 3.95 14.10 12.04 85.97 79.84 5.82 14.15 1.11 4.77 2.84 0.00
122 25 25 younger Female Low 3 No Yes BTT HMII alive Alive s/p OHT 3 124056 80873 65.19 95.41 0.37 14.36 90.47 5.98 0.39 0.60 41.84 4.26 51.08 2.81 18.82 35.29 43.53 86.97 0.10 11.32 1.10 75.49 12.12 3.80 14.94 0.24 0.88 3.25 0.00
123 25 25 younger Female Low 3 No Yes BTT HMII alive Alive s/p OHT 5 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA
124 25 25 younger Female Low 3 No Yes BTT HMII alive Alive s/p OHT 8 87840 57990 66.02 95.60 0.11 15.80 89.00 9.49 1.56 5.02 45.89 7.18 43.54 3.39 6.10 19.51 56.71 84.23 3.14 9.95 10.70 72.13 52.73 7.06 17.53 0.74 3.13 5.13 0.13
125 25 25 younger Female Low 3 No Yes BTT HMII alive Alive s/p OHT 14 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA
126 25 25 younger Female Low 3 No Yes BTT HMII alive Alive s/p OHT 21 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA
127 27 62 older Male High 2 No NA BTT CMAG dead Died 0 105070 38521 36.66 98.39 47.84 12.88 60.82 39.18 11.08 2.89 33.87 29.43 26.68 10.01 19.72 21.92 2.99 59.35 14.64 20.23 3.45 81.40 46.10 24.47 24.27 24.04 11.00 17.02 1.51
128 27 62 older Male High 2 No NA BTT CMAG dead Died 1 162336 73080 45.02 99.08 49.35 13.95 74.24 25.76 7.77 3.84 45.21 19.33 28.85 6.61 19.16 23.45 0.81 65.34 14.40 13.50 3.17 86.68 71.39 23.26 17.70 15.21 6.93 13.29 0.88
129 27 62 older Male High 2 No NA BTT CMAG dead Died 3 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA
130 27 62 older Male High 2 No NA BTT CMAG dead Died 5 111264 60487 54.36 99.15 45.94 16.13 73.16 26.84 4.64 1.82 52.04 20.07 20.94 6.95 22.93 23.47 0.50 77.11 9.30 9.58 1.20 88.92 81.82 22.20 19.01 16.98 6.89 13.57 1.36
131 27 62 older Male High 2 No NA BTT CMAG dead Died 8 165870 67935 40.96 98.88 43.01 15.86 70.23 29.77 7.85 1.88 40.39 20.49 29.66 9.46 22.70 29.00 1.88 68.61 9.60 16.11 1.47 89.57 69.00 20.12 16.59 17.10 7.02 12.40 2.06
132 27 62 older Male High 2 No NA BTT CMAG dead Died 14 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA
133 27 62 older Male High 2 No NA BTT CMAG dead Died 21 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA
134 13 61 older Male High 1 Yes No BTT TAH alive Alive s/p OHT 0 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA
135 13 61 older Male High 1 Yes No BTT TAH alive Alive s/p OHT 1 87827 15751 17.93 76.38 31.60 12.17 77.46 22.54 6.35 2.53 50.34 20.22 27.05 2.39 19.68 7.62 19.05 75.55 7.38 9.49 0.71 94.26 89.19 11.68 17.96 18.78 6.97 10.86 12.46
136 13 61 older Male High 1 Yes No BTT TAH alive Alive s/p OHT 3 55539 13608 24.50 79.00 28.02 15.78 81.90 18.10 6.13 2.42 66.92 14.33 14.98 3.77 20.81 17.45 18.12 78.01 7.08 8.61 0.72 94.04 70.73 11.32 16.69 15.21 5.78 10.50 16.39
137 13 61 older Male High 1 Yes No BTT TAH alive Alive s/p OHT 5 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA
138 13 61 older Male High 1 Yes No BTT TAH alive Alive s/p OHT 8 295005 36785 12.47 94.58 36.55 9.14 86.32 13.68 2.45 1.82 37.01 12.52 49.18 1.29 16.24 4.71 12.47 8.36 1.73 6.64 0.81 84.78 46.55 12.52 9.28 5.94 1.73 4.47 2.49
139 13 61 older Male High 1 Yes No BTT TAH alive Alive s/p OHT 14 60695 20471 33.73 94.91 6.93 7.42 83.97 16.03 3.40 0.69 24.36 14.71 59.33 1.60 18.43 5.07 11.52 54.82 2.91 16.10 0.50 82.44 30.00 51.08 13.25 10.41 3.68 11.31 6.06
140 13 61 older Male High 1 Yes No BTT TAH alive Alive s/p OHT 21 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA
141 19 46 younger Male High 2 No NA DT HMII alive Alive 0 226762 25868 11.41 89.41 25.31 12.05 55.06 44.94 11.31 2.69 14.79 42.57 39.95 2.69 19.87 3.88 32.88 68.95 10.48 13.57 0.59 80.62 22.67 31.91 19.38 15.58 10.37 16.55 8.18
142 19 46 younger Male High 2 No NA DT HMII alive Alive 1 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA
143 19 46 younger Male High 2 No NA DT HMII alive Alive 3 244049 39386 16.14 94.94 40.46 13.23 40.93 59.07 13.36 3.17 8.33 54.90 32.28 4.49 18.52 4.21 23.83 55.18 13.87 19.39 1.44 70.53 35.67 33.62 33.47 22.86 15.26 25.81 5.11
144 19 46 younger Male High 2 No NA DT HMII alive Alive 5 344736 250121 72.55 89.83 7.54 3.81 45.84 54.16 3.96 1.53 13.39 52.70 32.18 1.72 67.14 2.92 2.44 74.68 6.81 13.91 0.21 63.33 58.02 33.05 30.94 19.83 13.96 26.74 0.22
145 19 46 younger Male High 2 No NA DT HMII alive Alive 8 216934 140093 64.58 96.37 4.78 7.22 22.49 77.51 13.49 0.64 7.22 67.61 15.17 10.00 35.88 7.82 17.22 51.28 39.40 6.56 1.33 62.59 58.06 66.67 64.59 53.00 50.26 63.78 4.97
146 19 46 younger Male High 2 No NA DT HMII alive Alive 14 215820 66785 30.94 92.54 17.20 6.01 25.88 74.12 9.15 1.45 3.09 71.72 22.44 2.74 65.43 3.42 0.04 69.38 15.93 8.85 0.74 50.58 24.07 52.78 48.88 32.28 28.19 44.04 0.04
147 19 46 younger Male High 2 No NA DT HMII alive Alive 21 670692 523014 77.98 96.05 5.07 2.64 23.61 76.39 4.11 0.49 4.79 73.53 18.68 3.00 42.40 2.72 4.49 71.95 20.81 5.51 0.45 48.22 44.62 60.13 60.26 39.07 36.82 56.38 1.49
148 2 81 older Male Low 3 No NA DT HMII dead Died 0 119377 77509 64.93 99.61 58.50 7.99 62.67 37.33 9.10 4.82 36.73 31.90 25.62 5.74 11.47 8.95 0.40 69.54 7.69 9.41 2.61 76.44 57.91 23.29 20.76 15.39 5.42 14.90 2.60
149 2 81 older Male Low 3 No NA DT HMII dead Died 1 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA
150 2 81 older Male Low 3 No NA DT HMII dead Died 3 96940 57658 59.48 99.70 55.52 9.21 72.15 27.85 3.85 3.82 48.41 21.75 23.49 6.35 12.10 16.04 0.28 75.30 3.72 6.65 2.11 80.52 67.33 15.80 15.23 6.71 1.32 8.86 0.26
151 2 81 older Male Low 3 No NA DT HMII dead Died 5 154373 73969 47.92 99.65 45.18 8.77 67.36 32.64 6.59 2.77 39.10 26.28 27.95 6.67 17.89 15.71 0.39 71.57 6.26 9.88 1.78 81.86 72.07 20.12 20.17 14.80 5.99 14.65 3.71
152 2 81 older Male Low 3 No NA DT HMII dead Died 8 155610 63375 40.73 99.51 38.42 12.40 71.69 28.31 4.36 2.62 37.82 23.43 33.50 5.24 17.37 14.92 0.60 65.04 2.80 11.23 2.54 83.55 37.56 15.55 15.45 9.55 2.66 10.91 0.28
153 2 81 older Male Low 3 No NA DT HMII dead Died 14 244245 115109 47.13 99.47 47.40 9.37 67.50 32.50 3.99 2.08 50.08 26.01 17.22 6.68 15.34 15.25 0.23 77.86 3.21 10.49 1.48 82.13 59.19 21.45 19.77 14.45 2.57 14.94 0.94
154 2 81 older Male Low 3 No NA DT HMII dead Died 21 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA
155 9 60 younger Female High 2 Yes Yes BTT PVAD dead Died 0 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA
156 9 60 younger Female High 2 Yes Yes BTT PVAD dead Died 1 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA
157 9 60 younger Female High 2 Yes Yes BTT PVAD dead Died 3 116462 41076 35.27 95.44 33.79 25.24 84.51 15.49 2.92 0.99 45.34 13.19 39.12 2.36 17.56 8.75 19.73 79.35 5.17 10.80 0.71 90.04 29.59 10.16 6.81 8.21 3.37 4.86 4.47
158 9 60 younger Female High 2 Yes Yes BTT PVAD dead Died 5 222650 85649 38.47 98.40 32.09 19.82 77.54 22.46 5.02 1.10 43.96 19.20 33.50 3.34 17.47 9.77 15.63 71.89 6.68 14.08 0.70 86.49 27.87 13.04 9.84 12.30 4.35 7.98 6.39
159 9 60 younger Female High 2 Yes Yes BTT PVAD dead Died 8 102274 63057 61.65 97.73 27.89 20.66 73.75 26.25 7.33 3.45 35.79 21.92 37.73 4.56 9.97 8.20 16.96 63.96 2.40 11.16 3.07 73.97 5.92 16.69 17.77 11.74 4.90 12.19 6.09
160 9 60 younger Female High 2 Yes Yes BTT PVAD dead Died 14 133530 81665 61.16 96.46 22.03 16.15 35.30 64.70 13.74 2.33 8.48 52.28 26.37 12.87 5.29 5.79 19.15 47.48 5.65 17.83 5.43 39.88 6.08 52.08 62.11 37.45 21.95 50.15 3.84
161 9 60 younger Female High 2 Yes Yes BTT PVAD dead Died 21 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA
162 1 65 older Male High 2 No NA BTT HMII alive Alive s/p OHT 0 169154 35496 20.98 99.53 25.37 19.82 86.02 13.98 1.26 2.54 57.81 11.74 28.06 2.39 21.74 14.36 0.72 81.05 2.86 13.60 0.58 95.22 84.83 10.47 4.33 8.50 1.39 3.13 1.09
163 1 65 older Male High 2 No NA BTT HMII alive Alive s/p OHT 1 63082 9915 15.72 99.26 32.45 26.26 90.06 9.94 0.89 2.09 54.27 7.70 35.71 2.32 31.10 20.47 1.57 84.06 2.59 10.79 0.26 97.02 92.59 7.50 3.13 6.42 1.32 2.44 1.49
164 1 65 older Male High 2 No NA BTT HMII alive Alive s/p OHT 3 75921 21721 28.61 99.31 24.86 33.01 86.38 13.62 1.54 1.26 45.74 10.98 40.44 2.84 31.80 18.04 1.15 86.21 4.82 6.56 0.24 90.41 73.33 10.00 7.25 10.12 3.22 5.67 2.05
165 1 65 older Male High 2 No NA BTT HMII alive Alive s/p OHT 5 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA
166 1 65 older Male High 2 No NA BTT HMII alive Alive s/p OHT 8 213808 36002 16.84 99.19 35.95 14.55 67.94 32.06 4.06 2.17 27.92 28.92 39.64 3.52 20.31 9.10 1.33 68.69 7.10 20.42 1.88 87.38 44.25 10.78 11.12 19.15 5.54 7.35 1.07
167 1 65 older Male High 2 No NA BTT HMII alive Alive s/p OHT 14 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA
168 1 65 older Male High 2 No NA BTT HMII alive Alive s/p OHT 21 106970 31867 29.79 99.18 42.36 15.02 84.69 15.31 1.94 2.11 55.41 13.14 29.13 2.32 20.22 12.88 2.08 83.21 5.20 9.50 1.10 94.44 73.00 9.04 6.99 9.22 2.80 4.78 1.44
169 26 49 younger Male Low 3 No NA DT HMII alive Alive 0 196315 122053 62.17 95.37 60.66 22.66 91.10 8.90 0.45 4.95 85.57 6.30 5.42 2.71 13.13 28.32 20.05 86.32 2.45 5.42 0.96 98.68 94.19 2.50 2.96 4.63 1.24 0.33 0.89
170 26 49 younger Male Low 3 No NA DT HMII alive Alive 1 91909 37622 40.93 96.10 43.22 38.85 95.48 4.52 0.14 2.19 85.07 3.09 10.33 1.51 21.03 27.23 9.08 88.84 1.13 3.91 0.23 98.77 88.27 1.16 1.16 2.34 0.38 0.21 0.45
171 26 49 younger Male Low 3 No NA DT HMII alive Alive 3 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA
172 26 49 younger Male Low 3 No NA DT HMII alive Alive 5 153762 86281 56.11 95.83 65.54 24.24 91.12 8.88 0.65 2.84 81.43 6.30 9.62 2.65 21.14 28.73 15.89 83.00 1.97 6.74 0.36 98.22 93.16 3.20 2.29 5.47 1.11 0.77 1.56
173 26 49 younger Male Low 3 No NA DT HMII alive Alive 8 82406 47485 57.62 92.71 65.75 17.46 91.79 8.21 1.08 1.99 76.35 5.70 15.41 2.54 20.56 26.95 11.99 78.67 1.35 7.97 0.28 97.55 85.62 2.65 2.56 5.19 1.18 0.86 1.79
174 26 49 younger Male Low 3 No NA DT HMII alive Alive 14 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA
175 26 49 younger Male Low 3 No NA DT HMII alive Alive 21 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA
176 7 49 younger Male Low 3 No No BTT HVAD alive Alive s/p OHT 0 89251 65181 73.03 76.76 84.53 1.15 74.65 25.35 1.91 1.39 55.03 22.40 19.62 2.95 15.65 6.80 25.85 70.49 0.87 23.26 0.23 83.16 25.00 8.85 5.03 11.63 1.56 2.95 3.08
177 7 49 younger Male Low 3 No No BTT HVAD alive Alive s/p OHT 1 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA
178 7 49 younger Male Low 3 No No BTT HVAD alive Alive s/p OHT 3 375167 234817 62.59 98.46 60.29 10.18 87.72 12.28 0.46 0.48 68.54 9.90 19.03 2.54 30.58 19.69 15.54 72.77 0.13 20.35 0.03 92.56 36.28 3.75 2.70 9.17 1.19 1.27 0.63
179 7 49 younger Male Low 3 No No BTT HVAD alive Alive s/p OHT 5 256306 162176 63.27 93.82 68.43 8.45 85.45 14.55 0.70 0.53 71.99 11.98 13.37 2.66 32.41 17.96 12.46 69.74 0.41 24.63 0.02 95.72 44.12 4.47 2.23 12.99 1.30 1.20 0.77
180 7 49 younger Male Low 3 No No BTT HVAD alive Alive s/p OHT 8 463136 330714 71.41 98.79 70.51 7.30 87.51 12.49 1.78 0.58 69.60 10.61 17.82 1.97 29.83 14.55 12.59 75.03 0.15 21.61 0.07 93.59 30.94 4.05 3.07 10.00 1.08 1.35 0.62
181 7 49 younger Male Low 3 No No BTT HVAD alive Alive s/p OHT 14 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA
182 7 49 younger Male Low 3 No No BTT HVAD alive Alive s/p OHT 21 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA
183 12 38 younger Male High 2 Yes Yes BTT TAH dead Died s/p OHT 0 128451 60927 47.43 96.82 60.77 4.70 77.26 22.74 2.17 1.95 55.58 18.40 21.54 4.47 27.86 18.89 15.33 69.90 0.94 24.40 0.14 70.73 1.85 8.01 8.66 20.21 5.45 3.32 0.39
184 12 38 younger Male High 2 Yes Yes BTT TAH dead Died s/p OHT 1 142796 22573 15.81 80.67 47.31 2.28 63.37 36.63 9.16 6.51 26.02 33.49 37.11 3.37 38.13 7.50 13.13 53.25 5.78 26.27 1.57 40.24 0.00 27.71 22.17 29.16 18.80 15.66 8.11
185 12 38 younger Male High 2 Yes Yes BTT TAH dead Died s/p OHT 3 157167 38008 24.18 93.47 34.86 3.95 69.71 30.29 3.92 3.92 33.64 26.30 35.78 4.28 39.54 11.49 14.94 66.86 2.85 24.31 1.04 64.50 7.27 21.60 20.53 27.66 14.54 14.18 2.12
186 12 38 younger Male High 2 Yes Yes BTT TAH dead Died s/p OHT 5 121823 23097 18.96 93.48 2.51 2.87 99.52 0.48 0.00 0.00 0.97 0.48 98.55 0.00 50.00 25.00 25.00 94.35 0.00 2.58 0.00 0.16 0.00 17.45 87.40 0.00 0.16 18.26 0.00
187 12 38 younger Male High 2 Yes Yes BTT TAH dead Died s/p OHT 8 196515 88579 45.07 85.54 17.17 3.28 59.38 40.62 3.21 1.41 35.44 35.28 23.87 5.42 62.85 12.32 3.71 66.05 4.38 23.22 0.27 74.53 31.43 25.51 28.12 39.78 25.79 21.57 0.79
188 12 38 younger Male High 2 Yes Yes BTT TAH dead Died s/p OHT 14 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA
189 12 38 younger Male High 2 Yes Yes BTT TAH dead Died s/p OHT 21 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA
190 17 68 older Male Low 3 No NA DT HMII dead Died 0 147997 54649 36.93 91.75 79.63 7.62 74.86 25.14 0.60 3.45 62.45 22.87 12.30 2.38 45.98 9.28 13.61 74.33 2.67 21.19 0.84 91.31 90.15 3.58 2.25 21.79 1.36 0.58 0.34
191 17 68 older Male Low 3 No NA DT HMII dead Died 1 177687 56400 31.74 97.13 69.76 12.60 81.83 18.17 0.65 1.61 55.77 16.13 26.02 2.09 53.19 10.70 11.57 82.92 1.38 13.98 0.28 89.83 85.59 3.78 1.85 14.65 1.30 0.68 0.18
192 17 68 older Male Low 3 No NA DT HMII dead Died 3 233155 67140 28.80 98.44 74.89 5.32 81.96 18.04 1.00 1.88 49.03 16.59 32.90 1.48 49.92 7.20 12.83 83.44 1.39 12.98 0.14 89.70 69.70 4.58 1.62 13.89 1.08 1.08 0.17
193 17 68 older Male Low 3 No NA DT HMII dead Died 5 99257 29455 29.68 97.33 62.48 4.73 80.60 19.40 1.84 1.25 45.06 18.36 35.25 1.33 44.61 6.32 12.27 82.89 0.88 13.20 0.09 83.55 35.29 7.23 3.54 14.75 2.29 3.02 1.20
194 17 68 older Male Low 3 No NA DT HMII dead Died 8 76358 18702 24.49 97.32 29.48 11.10 86.29 13.71 2.43 0.50 37.92 12.13 48.32 1.63 46.45 11.70 11.35 83.96 0.20 10.50 0.06 57.82 50.00 9.95 29.60 10.20 0.64 9.36 0.80
195 17 68 older Male Low 3 No NA DT HMII dead Died 14 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA
196 17 68 older Male Low 3 No NA DT HMII dead Died 21 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA 
df.temp <- df
colnames(df.temp) <- make.names(colnames(df), unique = T)
invisible(suppressWarnings(suppressMessages(ggpairs(df.temp, 
                                          mapping = aes(color = Survival), 
                                          columns = colnames(df.temp)[c(2,4,6,7,8,9,10,11)]) 
                                    )))

Correlation Analysis

require(pheatmap, quietly = T)
require(RColorBrewer, quietly = T)
r <- cor(df[,c(2,14:42)], use = "p")
pheatmap(r, 
         color = colorRampPalette(rev(brewer.pal(n = 7, name = "RdBu")))(100),
         breaks = seq(-1, 1, length.out = 100),
         fontsize = 6,
         cutree_rows = 5,
         cutree_cols = 5
         )

Principal Component Analysis

We identified large variability between individual patients, as well as device types.

suppressMessages(require(ggbiplot, quietly = T))
require(ggsci, quietly = T)

# Efron's double standardization
double_standardize <- function(x, niter = 100) {
    for(i in 1:niter) x <- t(scale(t(scale(x))))
    return(as.data.frame(x))
}

isna <- unique(unlist(apply(df[,14:42], 2, function(x) which(is.na(x)))))
pca <- prcomp(double_standardize(df[-isna, 14:42]), center = TRUE, scale. = TRUE)

colorfun <- function(grouping, ...){
    if(nlevels(factor(grouping)) > 10) scale_color_discrete(...)
    if(nlevels(factor(grouping)) <=10) scale_color_d3(...)
} 

plots.pca <- lapply(names(df)[1:17], function(this_var){
    this_groups <- df[-isna, this_var]
    if(is.numeric(this_groups)) this_groups <- cut(this_groups, 4)
    
    ggbiplot(pca,
             groups = this_groups,
             ellipse = TRUE,
             alpha = 0.3,
             varname.size = 1.2) + 
        colorfun(this_groups, name = this_var) +
        ggtitle(paste0(this_var, " variability")) +
        theme_classic() 
})

names(plots.pca) <- names(df)[1:17]
plots.pca$PatientID

plots.pca$`Device Type`

# for(ii in 1:length(plots.pca)) suppressWarnings(print(plots.pca[[ii]]))

Device Types

We analyzed the differences between device types using Fisher’s exact test. The following tables are statistically significant (q<0.05).

isfactor <- which(sapply(df, is.factor))[-1]
contingency <- lapply(isfactor, function(this_factor) table(df[,this_factor], df$`Device Type`))

fisher.p <- sapply(contingency, function(this_table){
  f <- fisher.test(this_table, simulate.p.value = T, B = 10000)
  f$p.value
})

contingency[which(p.adjust(fisher.p, method = "BH") < 0.05)]
## $AgeGreater60
##          
##           CMAG HMII HVAD PVAD TAH
##   younger    0   56    7   21   7
##   older      7   84    7    0   7
## 
## $Sex
##         
##          CMAG HMII HVAD PVAD TAH
##   Female    0   35    0   14   0
##   Male      7  105   14    7  14
## 
## $LowIntermacs
##       
##        CMAG HMII HVAD PVAD TAH
##   Low     0   63   14    0   0
##   High    7   77    0   21  14
## 
## $InterMACS
##    
##     CMAG HMII HVAD PVAD TAH
##   1    0    7    0    0   7
##   2    7   70    0   21   7
##   3    0   56   14    0   0
##   4    0    7    0    0   0
## 
## $RVAD
##      
##       CMAG HMII HVAD PVAD TAH
##   No     7  105   14    0   0
##   Yes    0   35    0   21  14
## 
## $Sensitized
##      
##       CMAG HMII HVAD PVAD TAH
##   No     0   42    7    0   7
##   Yes    0   28    7    7   7
## 
## $`VAD Indication`
##      
##       CMAG HMII HVAD PVAD TAH
##   BTT    7   98   14   21  14
##   DT     0   42    0    0   0
## 
## $`Device Type`
##       
##        CMAG HMII HVAD PVAD TAH
##   CMAG    7    0    0    0   0
##   HMII    0  140    0    0   0
##   HVAD    0    0   14    0   0
##   PVAD    0    0    0   21   0
##   TAH     0    0    0    0  14
## 
## $Survival
##        
##         CMAG HMII HVAD PVAD TAH
##   alive    0   98   14    7   7
##   dead     7   42    0   14   7
## 
## $Outcome
##                
##                 CMAG HMII HVAD PVAD TAH
##   Alive            0   28    0    0   0
##   Alive s/p OHT    0   70   14    7   7
##   Died             7   35    0    7   0
##   Died post OHT    0    7    0    0   0
##   Died s/p OHT     0    0    0    7   7

We analyzed the differences between device types using a mixed effect model.

suppressMessages(require(lmerTest, quietly = T))
suppressMessages(require(car, quietly = TRUE))

df.device <- df
colnames(df.device) <- make.names(colnames(df), unique = T)

varnames <- colnames(df.device)[14:42]
models.device <- lapply(varnames, function(this_var){
  this_formula <- as.formula(paste0(this_var, " ~ Device.Type * factor(Time) + (1|PatientID)"))
  invisible(suppressMessages(this_model <- lmer(this_formula, data = df.device)))
  this_anova <- Anova(this_model, type = 2)
  pvals <- this_anova$`Pr(>Chisq)`[c(1,3)]
  return(list(model = this_model,
              pvals = pvals))
})
names(models.device) <- colnames(df)[14:42]

pvals <- do.call(rbind, lapply(models.device, function(x) x$pvals))
rownames(pvals) <- varnames
colnames(pvals) <- c("Device", "Device:factor(Time)")

qBH <- matrix(p.adjust(pvals, method = "BH"), nrow = nrow(pvals))
rownames(qBH) <- colnames(df)[14:42]
colnames(qBH) <- colnames(pvals)

sigvars <- apply(apply(qBH, 2, function(x) x<=0.1), 1, function(x) sum(x) > 0)
sig.qtable <- qBH[sigvars,][order(qBH[sigvars,2]),]

kable(sig.qtable, 
      digits = 10,
      row.names = T,
      caption = "Significant device-type q-values") %>%
    kable_styling(bootstrap_options = c("striped", "hover", "condensed", "responsive"),
                  font_size = 10) %>%
    scroll_box(width = "100%", height = "300px")
Significant device-type q-values
Device Device:factor(Time)
CD19+CD5+ 0.18837680 0.0000000002
CD27+IgD- switched memory 0.35405042 0.0000058050
CD19+CD27+ 0.57707197 0.0000518816
CD27-IgD- switched memory 0.57707197 0.0000518816
CD19+CD11b+ 0.65950106 0.0013452317
CD27-IgD+ mature naive 0.07734532 0.0026478333
CD19CD24hiCD38-memory 0.97000494 0.0100899431
CD19+24dim38dim naive mature 0.99997840 0.0570900512
CD19+CD27+CD24hi 0.97000494 0.0666230567

Timecourse

require(reshape2, quietly = T)
df.long <- melt(df, id.vars = colnames(df)[1:13])
groups <- make.names(c("Device Type"))
names(df.long) <- make.names(names(df.long))

invisible(suppressMessages(require(Hmisc, quietly = T)))
stat_sum_df <- function(fun, geom="errorbar", ...) {
  stat_summary(fun.data = fun, geom = geom, width = 1, ...)
}

plots.ts <- lapply(rownames(sig.qtable), function(this_var){
    lapply(groups, function(this_groups){
        ggplot(subset(df.long, df.long$variable == this_var)) +
            aes(x = Time, y = value, group = PatientID) +
            aes_string(color = this_groups, fill = this_groups) +
            geom_line(alpha = 0) + 
            geom_point(alpha = 0) + 
            stat_summary(fun.y = mean, aes_string(group = this_groups), geom=c("point"), position = position_dodge(.5)) + 
        stat_summary(fun.y = mean, aes_string(group = this_groups), geom=c("line"), position = position_dodge(.5)) + 
            stat_sum_df(function(x) mean_cl_boot(x, conf.int = 0.68), mapping = aes_string(group = this_groups), position = position_dodge(.5)) + 
            #stat_smooth(aes_string(group = this_groups), method = "loess", span = 1) +
            scale_color_d3() + scale_fill_d3() +
            xlab("Time (days after surgery)") +
            ylab(this_var) + 
            ggtitle(paste(this_var)) +
            theme_classic()
    })
})
names(plots.ts) <- rownames(sig.qtable)

for(ii in c(1:length(plots.ts))){
  for(jj in 1:length(plots.ts[[ii]])){
    sumtable <- suppressMessages(summary(models.device[[rownames(sig.qtable)[ii]]]$model))
    sumtable <- sumtable$coefficients[-1, c(4:5)] # drop intercept
    sigsum <- sumtable[sumtable[,2] <= 0.05, , drop = F]
    print(sigsum)
    suppressWarnings(print(plots.ts[[ii]][[jj]]))
  }
}
##                                 t value     Pr(>|t|)
## Device.TypePVAD:factor(Time)3 -3.212790 1.985064e-03
## Device.TypeTAH:factor(Time)5   5.597892 4.249332e-07

##                                 t value     Pr(>|t|)
## Device.TypeHVAD:factor(Time)1  2.193867 3.164541e-02
## Device.TypePVAD:factor(Time)3 -4.506401 2.595755e-05

##                                 t value     Pr(>|t|)
## Device.TypeHVAD:factor(Time)1  2.288402 2.520393e-02
## Device.TypePVAD:factor(Time)3 -4.140293 9.549563e-05

##                                  t value     Pr(>|t|)
## factor(Time)14                  2.658002 9.549567e-03
## Device.TypeTAH:factor(Time)5    4.417748 3.766149e-05
## Device.TypeHMII:factor(Time)14 -2.262837 2.647667e-02
## Device.TypeHVAD:factor(Time)14 -2.248730 2.747890e-02
## Device.TypePVAD:factor(Time)14 -2.015937 4.729750e-02

##                                  t value     Pr(>|t|)
## factor(Time)14                  5.663951 2.822395e-07
## factor(Time)21                  2.286686 2.529833e-02
## Device.TypeHMII:factor(Time)3  -2.083219 4.087800e-02
## Device.TypePVAD:factor(Time)3  -2.149256 3.501689e-02
## Device.TypeHMII:factor(Time)14 -5.250946 1.469192e-06
## Device.TypeHVAD:factor(Time)14 -4.341077 4.591232e-05
## Device.TypePVAD:factor(Time)14 -2.999221 3.710150e-03

##                                  t value     Pr(>|t|)
## factor(Time)14                 -3.556174 6.728955e-04
## Device.TypeTAH:factor(Time)1   -2.304827 2.419980e-02
## Device.TypeTAH:factor(Time)5   -4.252348 6.589494e-05
## Device.TypeTAH:factor(Time)8   -2.129620 3.678382e-02
## Device.TypeHMII:factor(Time)14  2.953963 4.249260e-03
## Device.TypeHVAD:factor(Time)14  2.846370 5.784388e-03
## Device.TypePVAD:factor(Time)14  2.624952 1.059141e-02

##                               t value   Pr(>|t|)
## Device.TypeHVAD:factor(Time)1 2.07174 0.04206401

##                                 t value    Pr(>|t|)
## Device.TypePVAD:factor(Time)3 -2.848022 0.005697037

##                                t value   Pr(>|t|)
## Device.TypeHVAD:factor(Time)1 2.218908 0.02978656

Timecourse

require(reshape2, quietly = T)
df.long <- melt(df, id.vars = colnames(df)[1:13])


groups <- make.names(c("AgeGreater60", 
                 "Sex",
                 "LowIntermacs",
                 "RVAD", 
                 "Sensitized",
                 "VAD Indication", 
                 #"Device Type", 
                 "Survival",
                 "Outcome"))

names(df.long) <- make.names(names(df.long))

plots.ts <- lapply(unique(df.long$variable), function(this_var){
    lapply(groups, function(this_groups){
        ggplot(subset(df.long, df.long$variable == this_var)) +
            aes(x = Time, y = value, group = PatientID) +
            aes_string(color = this_groups, fill = this_groups) +
            geom_line(alpha = .1) + 
            geom_point(alpha = .1) + 
            stat_smooth(aes_string(group = this_groups), method = "loess", span = 1) +
            scale_color_aaas() + scale_fill_aaas() +
            xlab("Time (days after surgery)") +
            ylab(this_var) + 
            ggtitle(paste(this_var)) +
            theme_classic()
    })
})
names(plots.ts) <- unique(df.long$variable)

# for(ii in c(1:length(plots.ts))){
#     for(jj in 1:length(plots.ts[[ii]])){
#         suppressWarnings(print(plots.ts[[ii]][[jj]]))
#     }
# }

Statistical Tests

suppressMessages(require(lmerTest, quietly = TRUE))
suppressMessages(require(car, quietly = TRUE))
require(reshape2, quietly = TRUE)

df.lmer <- df
names(df.lmer) <- make.names(names(df.lmer), unique = TRUE)

groupvars.ix <- c(3,4,5,7,8,9,11)
groupvars <- names(df.lmer)[groupvars.ix]

bcells.ix <- c(14:42)
bcells <- names(df.lmer)[bcells.ix]

pvals <- lapply(groupvars, function(this_groupvar){
    these_pvalues <- lapply(bcells, function(this_bcell){
        this_formula <- as.formula(paste0(this_bcell, " ~ ", this_groupvar, 
                                          " * factor(Time) + (1|PatientID)"))
        suppressMessages(suppressWarnings(this_model <- lmer(this_formula, data = droplevels(df.lmer))))
        this_anova <- Anova(this_model, type = 2)
        this_pvalues <- this_anova$`Pr(>Chisq)`
        names(this_pvalues) <- rownames(this_anova)
        return(this_pvalues)
    })
    pvalues <- do.call(rbind, these_pvalues)
    rownames(pvalues) <- bcells
    return(pvalues)
})
names(pvals) <- groupvars
pvals.matrix <- do.call(cbind, lapply(pvals, function(this_pval) this_pval[,c(1,3)]))

# Benjamini Hochberg
# qBH <- matrix(p.adjust(as.numeric(pvals.matrix), 
#                        method = "BH"), 
#               nrow = nrow(pvals.matrix), 
#               ncol = ncol(pvals.matrix), 
#               byrow = F) 
# rownames(qBH) <- rownames(pvals.matrix)
# colnames(qBH) <- colnames(pvals.matrix)
# rownames(qBH) <- names(df)[bcells.ix]
# qvalsBH.df <- melt(qBH)
# colnames(qvalsBH.df) <- c("B-cell", "parameter", "qvalue")
# qvalsBH.df.ranked <- qvalsBH.df[order(qvalsBH.df$qvalue, decreasing = F),]
# qvalsBH.df.ranked[qvalsBH.df.ranked$qvalue <= 0.3,]

# Local FDR
require(fdrtool, quietly = T)
invisible(suppressMessages(fdrobj <- fdrtool(as.numeric(pvals.matrix), statistic = "pvalue", plot = F)))
## Step 1... determine cutoff point
## Step 2... estimate parameters of null distribution and eta0
## Step 3... compute p-values and estimate empirical PDF/CDF
## Step 4... compute q-values and local fdr
qvals.matrix <- matrix(fdrobj$q, nrow = nrow(pvals.matrix), ncol = ncol(pvals.matrix), byrow = F)
rownames(qvals.matrix) <- rownames(pvals.matrix)
colnames(qvals.matrix) <- colnames(pvals.matrix)
rownames(qvals.matrix) <- names(df)[bcells.ix]
qvals.df <- melt(qvals.matrix)
colnames(qvals.df) <- c("B-cell", "parameter", "qvalue")
qvals.df.ranked <- qvals.df[order(qvals.df$qvalue, decreasing = F),]
shortlist <- qvals.df.ranked[qvals.df.ranked$qvalue <= 0.3,]


kable(shortlist, 
      digits = 3,
      row.names = T,
      caption = "Significant results") %>%
    kable_styling(bootstrap_options = c("striped", "hover", "condensed", "responsive"),
                  font_size = 10) %>%
    scroll_box(width = "100%", height = "300px")
Significant results
B-cell parameter qvalue
227 CD19+CD11b+ RVAD:factor(Time) 0.037
145 CD19+27+IgD-38++IgG ASC LowIntermacs 0.180
3 lymph AgeGreater60 0.202
197 CD268 of +27-38++transitional RVAD 0.203
155 CD27-38++ transitional LowIntermacs:factor(Time) 0.206
101 CD27+IgD+ unswitched memory Sex:factor(Time) 0.229
321 num lymph VAD.Indication:factor(Time) 0.240
103 CD27+IgD+IgM+ nonswitched memory Sex:factor(Time) 0.251 
require(stringr, quietly = T)
siggroups <- sapply(str_split(shortlist$parameter, ":"), function(x) x[1])
for(ii in 1:nrow(shortlist)){
    this_group <-siggroups[ii]
    suppressWarnings(print(plots.ts[[shortlist$`B-cell`[ii]]][[which(groups == this_group)]]))
}